So to start I have a 2006 TL AT with navi and tpms. Here soon I'll be replacing the ECU with an 08 TL AT ECU. I can't find an ECU harness for the automatic transmission.
does anybody have the pinout for both of them, or possibly be able to tell me which pins need moved and where?

 

Get yourself service manuals.
This should be 2004-2006: https://acurazine.com/forums/third-g.../#post15344256
This is for 2007-2008: https://acurazine.com/forums/3g-tl-p.../#post16101585

ECM Connectors for 2007-2008 TL:


ECM Connectors for 2004-2006:

 

06 and 08 have different trans. 06 is 3 switches vs 4 for 07-08

 

so what will happen if I put the computer into my 06 will the transmission have problems?

 

if you’re asking this, one must ask why you are wanting to put in an 08 ECU in an 06? Did your ECU go bad? Are you trying to do something that an 08 ECU can that an 06 cannot?

 

yes the 06 ECU does work perfectly fine but what the 06 AT ECU cannot do is get tuned by a hondata flashpro but the 06 MT ECU can be tuned and so can the 08 AT ECU

 

What is it you hope to gain from such a swap and a tune?

 

I'm planning on dropping a turbo into it and bigger injectors so I'll need to tune it so it doesn't run lean. I'll only be running low psi but it'll still need tuned

 

Ummm, sorry to be the bearer of bad news, but you have the wrong car. The transmission in your car is barely able to deal with the power the engine is already putting out, adding a turbocharger will turn that thing into toast in pretty short order. As for the turbocharging itself, do you realize you're dealing with a V6 engine? Are you planning on running a turbo off of only one exhaust collector, or running two turbos, one for each collector, or relocating the exhaust plumbing so you can run one turbo off of the combined exhaust? What about the intercooler plumbing?